This question could not have come at a better time, I'm in fact working on exactly this topic since I got from my wife a nice 3D printer for Xmas :)
I already designed 2 chassis as prototypes, final plan is to release them to thingiverse as open source blueprints for 3D chassis. Currently I place the micro USB female breakout port which comes delivered with all Stardust V2 boards in the chassis, so you just need to remove the pommel to access it.
More importantly I'm now debating the option to include a mini USB breakout, which is mechanically more robust than a micro USB, which would also solve some of your concerns.
I'm currently shipping Stardust V2 boards with this breakout board:
10pcs MICRO-B USB Buchse Anschluss Connector Breakout Board Sockel Arduino |I consider this one as replacement if one wants an mini USB:
5x Mini-USB-Board Mini-USB-Modul Mini RGB Breakout Board für Arduino Pi Rot |If you want to place the USB breakout board to the outside of the saber for easy access, you can do that as well, not more difficult than putting a 21mm RC port, in fact a USB port is smaller. If you prefer cylindrical port, you can follow jbkuma's proposal.
For one of my TCSS sabers I'm planning to make a custom clamp box where the USB access will be on the lower part of the clamp box, facing down, so not immediately visible but well accessible.
As a side not: I usually plan place for either a 5mm or 3mm LED as charge indicator, connected between CHR(+) and GND(-) of the Stardust board.
I will later on send some pics of my 3D chassis designs. And there is another guy who works with Stardust who came up with a splendid idea how to place the USB in the chasiss, I will include them too!!! Stay tuned!